Is cheese good or bad for the microbiome?

January 3, 2026 •

3 min read

According to a 2025 study in Applied and Environmental Microbiology, specific bacteria from cheese were shown to modulate the human gut, confirming its potential to influence our internal ecosystem. The question of whether cheese is good or bad for the microbiome is complex and depends heavily on the type and quantity consumed.

Quick Summary

The impact of cheese on the microbiome is nuanced. Certain fermented and aged cheeses contain beneficial probiotics, while high-fat or processed varieties may pose risks, especially for intolerant individuals. Moderation and mindful selection are key to harnessing potential benefits.

Key Points

Probiotics: Aged and fermented cheeses like Gouda and cheddar can introduce beneficial live bacteria to the gut, supporting a healthy microbiome.
Moderation is key: Due to its high fat and sodium content, consuming cheese in moderation is crucial for preventing negative health impacts, including potential gut inflammation.
Lactose consideration: Hard, aged cheeses are lower in lactose, making them easier for lactose-intolerant individuals to digest than softer, fresher options.
Choose wisely: Opt for high-quality, minimally processed cheeses and avoid processed cheese products which lack live cultures and are high in additives.
Pairing matters: Combine cheese with high-fiber foods like vegetables and whole grains to enhance digestive benefits and balance its nutritional content.
SCFAs production: The probiotics in cheese can lead to the production of short-chain fatty acids (SCFAs), which are vital for colon health.

The Dual Nature of Cheese for Gut Health

Cheese has a complex relationship with the gut microbiome. While the fermentation process can introduce probiotics beneficial for gut flora, other components like high saturated fat, sodium, and lactose can negatively affect the ecosystem for some individuals. Understanding this balance is important for informed dietary choices.

The Probiotic Perks: How Cheese Can Be Beneficial

Aged and fermented cheeses often contain probiotics like Lactobacillus and Bifidobacterium which support balanced gut flora and digestion. These bacteria produce SCFAs, such as butyrate, which nourish colon cells. Cheese also provides protein for gut lining repair and calcium, which can influence microbial composition.

The Potential Pitfalls: When Cheese Can Be Harmful

Potential risks of cheese include high saturated fat, which may alter the microbiome and contribute to inflammation. High sodium can also disrupt gut bacteria. For lactose-intolerant individuals, undigested lactose in cheese can cause digestive issues. Processed cheeses are often less beneficial, lacking live cultures and containing more additives and sodium.

The Microbiome Impact of Different Cheese Types

The type of cheese significantly influences its effect on gut health, with certain varieties offering more benefits.

Best Cheeses for Probiotic Support

Aged Gouda: May contain Lactobacillus and Lactococcus.
Aged Cheddar: Low in lactose and may have beneficial bacteria.
Feta: Contains Lactobacillus plantarum and is lower in lactose.
Cottage Cheese: Look for varieties with added “live and active cultures”.
Swiss Cheese: Contains Propionibacterium freudenreichii.

Cheeses to Consume in Moderation

Processed Cheese: Lacks live cultures and is high in sodium and additives.
Soft, Unaged Cheeses: Higher in lactose, potentially problematic for intolerant individuals.
High-Fat Cheeses (in excess): Can contribute to gut inflammation.

Comparison: Probiotic vs. Processed Cheese


Feature	Probiotic-Rich Cheese (e.g., Aged Gouda, Cheddar)	Processed Cheese (e.g., American Cheese Slices)
Probiotic Content	Yes, contains live and active cultures from aging.	No, typically lacks live cultures due to heat treatment.
Lactose Content	Low, as lactose is broken down during fermentation.	Variable, can be higher depending on processing.
Saturated Fat	Present, requires moderation.	Present, often higher in some varieties.
Sodium	Variable, aged cheeses can be high.	Often high due to added ingredients.
Additives	Minimal, especially in artisan varieties.	Significant, including emulsifiers and stabilizers.

How to Mindfully Consume Cheese for Microbiome Health

Incorporating cheese into a gut-healthy diet involves choosing aged, fermented, and minimally processed varieties and consuming them in moderation. Pairing cheese with fiber-rich foods can improve its nutritional balance and aid digestion. Individuals with lactose sensitivity may find aged or lower-lactose options more suitable. Using cheese as a flavor accent rather than a main dish helps manage portion sizes and intake of fat and sodium. A balanced diet, which can include cheese in moderation, is key to a diverse microbiome. Further reading on balancing your diet can be found in this Harvard Health guide: Is cheese a healthy source of probiotics?

Conclusion

Cheese's effect on the microbiome is not strictly good or bad; it's dependent on the type and how it's consumed. Aged and fermented cheeses can offer probiotics and nutrients for gut health, while high fat, sodium, and lactose in some cheeses may cause issues. Selecting aged and fermented options and eating cheese in moderation as part of a varied diet are the best ways to enjoy it while supporting your gut microbiome.

Frequently Asked Questions

Aged and fermented cheeses are generally best for gut health as they contain probiotics. Good options include aged Gouda, aged cheddar, Swiss, and feta. Some cottage cheeses may also contain added probiotics; check the label for "live and active cultures".

Yes, for some individuals. If you are lactose intolerant, undigested lactose from cheese can be fermented by gut bacteria, leading to bloating, gas, and abdominal pain. Hard, aged cheeses have lower lactose levels and are often better tolerated.

No, processed cheese is generally not beneficial for the microbiome. It lacks the live, active cultures found in aged cheeses due to heat treatment during processing and is typically higher in sodium and additives.

The relationship between cheese and inflammation is complex. While high saturated fat can be a concern, fermented dairy, including cheese, has shown neutral to beneficial effects on inflammation markers in many studies when consumed in moderation.

Certain types of cheese, especially those that are aged but not heat-treated after fermentation, can be a good source of probiotics. However, the amount and viability of probiotics can vary, so it's often not as potent as dedicated probiotic supplements or yogurt.

To benefit your gut, consume high-quality, aged cheeses in moderation. Pair them with fiber-rich foods like fruits, vegetables, and whole-grain crackers. This combination can help balance the meal and support overall digestive health.

In some cases, cheese can contribute to constipation, especially when consumed in large quantities due to its high fat content and lack of fiber. However, for some, the calcium and fermented nature of certain cheeses may have a different effect, highlighting the importance of individual tolerance and balanced consumption.